def beddb(filepath, uuid=None, **kwargs):
from clodius.tiles.beddb import tileset_info, tiles
return Tileset(uuid=uuid,
tileset_info=lambda: tileset_info(filepath),
tiles=lambda tids: tiles(filepath, tids),
**kwargs)
def dfpoints(df, x_col, y_col, uuid=None, **kwargs):
"""
Generate a tileset that serves 2d labelled points from a pandas
dataframe.
Parameters
----------
df: :class:`pandas.DataFrame`
The dataframe containining the data
x_col: str
The name of the column containing the x-coordinates
y_col: str
The name of the column containing the y-coordinates
uuid: str
The uuid of this tileset
Returns
-------
A tileset capapble of serving tiles from this dataframe.
"""
from clodius.tiles.points import tileset_info, tiles, format_data
tsinfo = tileset_info(df, x_col, y_col)
tiles_fn = lambda z, x, y, width=1, height=1: tiles(
df, x_col, y_col, tsinfo, z, x, y, width, height)
return Tileset(uuid=uuid,
tileset_info=lambda: tsinfo,
tiles=lambda tile_ids: format_data(
bundled_tiles_wrapper_2d(tile_ids, tiles_fn)),
datatype="scatter-point",
**kwargs)
def cooler(filepath, uuid=None, **kwargs):
from clodius.tiles.cooler import tileset_info, tiles
return Tileset(uuid=uuid,
tileset_info=lambda: tileset_info(filepath),
tiles=lambda tids: tiles(filepath, tids),
datatype="matrix",
**kwargs)
def bigbed(filepath, uuid=None, chromsizes=None, **kwargs):
from clodius.tiles.bigbed import tileset_info, tiles
return Tileset(
uuid=uuid,
tileset_info=lambda: tileset_info(filepath, chromsizes),
tiles=lambda tids: tiles(filepath, tids, chromsizes=chromsizes),
**kwargs)
def cooler(filepath, uuid=None):
return Tileset(
tileset_info=lambda: hgco.tileset_info(filepath),
tiles=lambda tids: hgco.tiles(filepath, tids),
uuid=uuid,
track_type="heatmap",
track_position="center",
)
def bigwig(filepath, uuid=None, chromsizes=None, **kwargs):
from clodius.tiles.bigwig import tileset_info, tiles
return Tileset(
uuid=uuid,
tileset_info=lambda: tileset_info(filepath, chromsizes),
tiles=lambda tids: tiles(filepath, tids, chromsizes=chromsizes),
datatype="vector",
**kwargs)
def multivec(filepath, uuid=None, **kwargs):
from clodius.tiles.multivec import tileset_info, tiles
return Tileset(
uuid=uuid,
tileset_info=lambda: tileset_info(filepath),
tiles=lambda tile_ids: tiles(filepath, tile_ids),
**kwargs
)
def mrmatrix(filepath, uuid=None, **kwargs):
from clodius.tiles.mrmatrix import tileset_info, tiles
f = h5py.File(filepath, "r")
return Tileset(
uuid=uuid,
tileset_info=lambda: tileset_info(f),
tiles=lambda tile_ids: tiles_wrapper_2d(
tile_ids, lambda z, x, y: format_dense_tile(tiles(f, z, x, y))),
datatype="matrix",
**kwargs)
def tiles(cls, tileset_dict, tids):
filetype = tileset_dict.get('filetype', "")
if filetype == "bam":
data = bam_tiles.tiles(
tileset_dict.datafile, tids,
index_filename=tileset_dict.index_filename
)
elif filetype == "cooler":
data = cooler_tiles.tiles(tileset_dict['datafile'], tids)
elif filetype == "bigwig":
data = bigwig_tiles.tiles(tileset_dict['datafile'], tids)
else:
data = {'error': f"Unknown tileset filetype: {filetype}"}
return data
def test_cooler_tiles():
filename = op.join('data', 'hic-resolutions.cool')
hgco.tiles(filename, ['x.0.0.0'])
def test_cooler_tiles():
filename = op.join("data", "hic-resolutions.cool")
hgco.tiles(filename, ["x.0.0.0"])